This is a summary of all "fixes" that I am aware of that other people have documented. I am assembling this in one place for convenience. All credit goes to the original authors!
I would like to clarify that this is for "fixes" that take care of apparent design deficiencies right out of the box. This is not a thread for "mods" like adding playfield toys or speaker upgrades. Please add whatever you find and I will try to keep this first post up to date.
1) Ball getting stuck on pop bumpers.
http://pinside.com/pinball/forum/topic/ball-getting-stuck-on-st
2) Improve flow (not necessary with software newer then 1.4), kickout consistency, slow warp ramp for consistency
http://pinside.com/pinball/forum/topic/star-trek-gameplay-tweaks
3) Reduce slingshot power to reduce airballs
http://pinside.com/pinball/forum/topic/star-trek-pro-getting-balls-stuck-in-slingshots
4) Reduce scratching of balls
http://pinside.com/pinball/forum/topic/star-trek-pinballs-getting-torn-up
5) Vengeance ship leaning
http://pinside.com/pinball/forum/topic/star-trek-vengeance-ship-leaning-and-alignment-fix
6) Adjust warp ramp, adjust kicker power, add urethane "rubbers" (See first comment of the article, which is directly from Steve Ritchie!)
http://www.pinballnews.com/games/startrek/index4.html
Fixes and adjustments from Steve Ritchie's comment are copied here:
The ST Warp Ramp exit is easily adjustable at the exit end on all models. There is a fixing screw with washers pinching the plastic ramp between them. A lateral slot has been designed into the ramp, and with the playfield pulled forward so that the "feet" of the playfield support brackets safely parked in the front molding tray, one can grasp and adjust the Warp Ramp exit with the left hand while loosening and tightening can be achieved with a long-ish #2 Phillips screwdriver with the right hand. There is an access port cut into the Beta Ramp edge and plastic just for this use.
While the ball is wild and speeds vary along the Warp Ramp, every ST model can be adjusted so that a nice feed to the upper right flipper can largely be attained. Some ST games need the adjustment and some don't.
I don't recommend the use of post sleeves on the mini posts in place of the rubber donuts. Sleeves have too little rebound for my tastes, and they don't belong on ST. "Says who?" Says The King! You can use sleeves, but I will laugh and jeer like the Black Knight when I see your game.
There are some great new urethane post, mini post and flipper rubbers (Super Bands) available from Marco that are super durable and provide great rebound. They are manufactured by C.U.E. led by Joe Scalleta, and come in a full range of colors and styles. I wish I knew about them and not sure they were even available before ST production; I would have specified them on all models. They show no wear at all after hundreds of fun plays in my testing.
...
There are new adjustments in the diagnostics to adjust kicker power for sling shots and the left eject.
...
7) Flashers too bright:
http://pinside.com/pinball/forum/topic/stern-star-trek-how-to-dim-flashers#post-1437743
8 ) Spotlight bulbs on slingshot repeatedly fall out of socket:
http://pinside.com/pinball/forum/topic/star-trek-slingshot-lamp-bulbs-continue-to-fall-out
9) Improve lighting uniformity of Warp ramp insignia
http://pinside.com/pinball/forum/topic/st-proprele-warp-ramp-insignia-lighting-mod-
10) Improve lighting uniformity of right Enterprise inserts
http://pinside.com/pinball/forum/topic/st-pro-two-right-enterprise-inserts-are-dim#post-1573036
11) On some machines, the Vengeance entrance opto does not work when the Vengeance magnet is energized. Fix by twisting the opto wires:
http://pinside.com/pinball/forum/topic/stern-star-trek-multiball-magnet/page/7#post-1601229
http://pinside.com/pinball/forum/topic/stern-star-trek-multiball-magnet/page/7#post-1603880
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12) Install service rails missing in Pro
http://pinside.com/pinball/forum/topic/has-anybody-installed-service-rails-on-a-star-trek-pro-yet